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Bacterial whole genome sequencing

Martin Wardle, Andre Mu, Steven Y C Tong
We describe a case of Streptococcus gallolyticus subsp pasteurianus meningitis, unusually occurring in a splenectomised patient and complicated by cerebral venous thrombosis. Following presentation with meningism and diagnosis and management of S. gallolyticus meningitis, the patient represented with a further four days of fevers and subsequently developed left sided paresthesias. Cerebral imaging revealed venous thrombus in the right frontal cortical veins and left sigmoid sinus. The patient recovered following four weeks of intravenous ceftriaxone and anticoagulation with enoxaparin and then warfarin...
April 12, 2018: International Journal of Infectious Diseases: IJID
Märt Roosaare, Mikk Puustusmaa, Märt Möls, Mihkel Vaher, Maido Remm
Background: Plasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make plasmid detection a complex problem. Results: We developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on k -mers and uses k -mer abundance to distinguish between plasmid and bacterial sequences...
2018: PeerJ
Adam M Blanchard, Keith A Jolley, Martin C J Maiden, Tracey J Coffey, Grazieli Maboni, Ceri E Staley, Nicola J Bollard, Andrew Warry, Richard D Emes, Peers L Davies, Sabine Tötemeyer
Dichelobacter nodosus ( D. nodosus ) is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of D. nodosus have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.) population and its relationship globally, is poorly understood. Numerous epidemiological methods are available for bacterial typing; however, few account for whole genome diversity or provide the opportunity for future application of new computational techniques...
2018: Frontiers in Microbiology
K Lisowska-Łysiak, P Dudko, M Kosecka-Strojek, J Walczak, P Wójcik, J Międzobrodzki
Staphylococci are very common human and animal pathogens. A variety of staphylococcal virulence determinates leads to vast range of infections. One of them is mastitis which is a common disease of the mammary glands. The incidence of this disease is widespread all over the world and depends on bacterial virulence and on prevention programs. The influence of mastitis on human health is not globally evaluated, however, in veterinary fields loses in milk production caused by bovine mastitis are a constant economic problem...
March 2018: Polish Journal of Veterinary Sciences
Kathy Raven, Beth Blane, Carol Churcher, Julian Parkhill, Sharon J Peacock
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality...
April 5, 2018: Microbial Genomics
Stefan Bletz, Sandra Janezic, Dag Harmsen, Maja Rupnik, Alexander Mellmann
Clostridium difficile , recently renamed to Clostridioides difficile , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, a highly discriminatory subtyping is necessary. Today, methods based on whole genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature is missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C...
April 4, 2018: Journal of Clinical Microbiology
Xi Guo, Min Wang, Lu Wang, Yao Wang, Tingting Chen, Pan Wu, Min Chen, Bin Liu, Lu Feng
Serotyping based on surface polysaccharide antigens is important for the clinical detection and epidemiological surveillance of pathogens. Polysaccharide gene clusters (PSgcs) are typically responsible for the diversity of bacterial surface polysaccharides. Through whole-genome sequencing and analysis, eight putative PSgc types were identified in 23 Enterobacter aerogenes strains from several geographic areas, allowing us to present the first molecular serotyping system for E. aerogenes . A conventional antigenic scheme was also established and correlated well with the molecular serotyping system that was based on PSgc genetic variation, indicating that PSgc-based molecular typing and immunological serology provide equally valid results...
2018: Frontiers in Microbiology
Shlomo E Blum, Robert J Goldstone, James P R Connolly, Maryline Répérant-Ferter, Pierre Germon, Neil F Inglis, Oleg Krifucks, Shubham Mathur, Erin Manson, Kevin Mclean, Pascal Rainard, Andrew J Roe, Gabriel Leitner, David G E Smith
Escherichia coli are major bacterial pathogens causing bovine mastitis, a disease of great economic impact on dairy production worldwide. This work aimed to study the virulence determinants of mammary pathogenic E. coli (MPEC). By whole-genome sequencing analysis of 40 MPEC and 22 environmental ("dairy-farm" E. coli [DFEC]) strains, we found that only the fec locus ( fecIRABCDE ) for ferric dicitrate uptake was present in the core genome of MPEC and that it was absent in DFEC genomes ( P < 0...
April 3, 2018: MBio
Misako Yajima, Kazufumi Ikuta, Teru Kanda
Herpesviruses have relatively large DNA genomes of more than 150 kb that are difficult to clone and sequence. Bacterial artificial chromosome (BAC) cloning of herpesvirus genomes is a powerful technique that greatly facilitates whole viral genome sequencing as well as functional characterization of reconstituted viruses. We describe recently invented technologies for rapid BAC cloning of herpesvirus genomes using CRISPR/Cas9-mediated homology-directed repair. We focus on recent BAC cloning techniques of Epstein-Barr virus (EBV) genomes and discuss the possible advantages of a CRISPR/Cas9-mediated strategy comparatively with precedent EBV-BAC cloning strategies...
April 3, 2018: Viruses
Andie S Lee, Elizabeth White, Leigh G Monahan, Slade O Jensen, Raymond Chan, Sebastiaan J van Hal
OBJECTIVETo describe the transmission dynamics of the emergence and persistence of vanA vancomycin-resistant enterococcus (VRE) in an intensive care unit (ICU) using whole-genome sequencing of patient and environmental isolates.DESIGNRetrospective cohort study.SETTINGICU in a tertiary referral center.PARTICIPANTSPatients admitted to the ICU over an 11-month period.METHODS VanA VRE isolated from patients (n=31) were sequenced using the Illumina MiSeq platform. Environmental samples from bed spaces, equipment, and waste rooms were collected...
April 3, 2018: Infection Control and Hospital Epidemiology
Mattia Palmieri, Stephane Schicklin, Andreu Coello Pelegrin, Sonia Chatellier, Christine Franceschi, Caroline Mirande, Yeon Joon Park, Alex van Belkum
The prevalence of multidrug-resistant gram-negative bacteria has continuously increased over the past few years; bacterial strains producing AmpC β-lactamases and/or extended-spectrum β-lactamases (ESBLs) are of particular concern. We combined high-resolution whole genome sequencing and phenotypic data to elucidate the mechanisms of resistance to cephamycin and β-lactamase in Korean Klebsiella pneumoniae strains, in which no AmpC-encoding genes were detected by PCR. We identified several genes that alone or in combination can potentially explain the resistance phenotype...
July 2018: Annals of Laboratory Medicine
Ananta N Panda, Samir Ranjan Mishra, Lopamudra Ray, Surajit Das, Gurdeep Rastogi, Ajit Kumar Pattanaik, Tapan Kumar Adhya, Mrutyunjay Suar, Vishakha Raina
moderately halophilic spore forming, motile, Gram-positive, rod-shaped bacterial strain designated as KGW1T was isolated from water sample of Chilika Lake and characterized taxonomically using polyphasic approach. The strain grew in the presence of 0-25% (w/v) NaCl in marine salt agar media, hydrolyzes casein, and gelatin and shows presence of alkaline proteases. The major cell wall menaquinone was MK7 and major cellular fatty acids were anteiso-C15:0 (44.89%), anteiso-C17:0 (6.18%), isoC15:0 (19.38%), and iso-C16:0 (7...
April 2018: Journal of Microbiology / the Microbiological Society of Korea
Ji Zhang, Yanwen Xiong, Lynn Rogers, Glen P Carter, Nigel French
Motivation: Large-scale whole-genome sequencing (WGS) dataset based studies are becoming increasingly common in pathogen surveillance and outbreak investigations. A highly discriminative and time-efficient bioinformatics tool is needed to transform large amounts of sequencing data into usable biological information. To replace the intuitive, yet inefficient, way of gene-by-gene allele calling algorithm, a new algorithm using genome-by-genome approach was developed. Results: Tests showed that the program equipped with the new algorithm achieved significant improvements in allele calling efficiency compared to a conventional gene-by-gene approach...
March 28, 2018: Bioinformatics
Maarten J Gilbert, Birgitta Duim, Linda van der Graaf-van Bloois, Jaap A Wagenaar, Aldert L Zomer
Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare...
March 1, 2018: Genome Biology and Evolution
Francesca Giordano, Maximilian R Stammnitz, Elizabeth P Murchison, Zemin Ning
Motivation: The recent technological advances in genome sequencing techniques have resulted in an exponential increase in the number of sequenced human and non-human genomes. The ever increasing number of assemblies generated by novel de novo pipelines and strategies demands the development of new software to evaluate assembly quality and completeness. One way to determine the completeness of an assembly is by detecting its Presence-Absence variations (PAV) with respect to a reference, where PAVs between two assemblies are defined as the sequences present in one assembly but entirely missing in the other one...
March 28, 2018: Bioinformatics
Emma Taylor, Shiranee Sriskandan, Neil Woodford, Katie L Hopkins
The emergence of 16S rRNA methyltransferases (16S RMTases) worldwide is a growing concern due to their ability to confer high-level resistance (MICs >256 mg/L) to all clinically-relevant aminoglycosides. As the occurrence of 16S RMTases in the United Kingdom has not been investigated to date, we screened 806 Enterobacteriaceae isolates displaying high-level aminoglycoside resistance (amikacin, gentamicin and tobramycin MICs ≥64, ≥32 and ≥32 mg/L, respectively) for 16S RMTases either by analysing whole-genome sequence (WGS) data (which were available for 449 isolates) or by PCR...
March 26, 2018: International Journal of Antimicrobial Agents
María Elisa Pavan, Esteban E Pavan, Stefanie P Glaeser, Claudia Etchebehere, Peter Kämpfer, María Julia Pettinari, Nancy I López
The genus Coprothermobacter (initially named Thermobacteroides) is currently placed within the phylum Firmicutes. Early 16S rRNA gene based phylogenetic studies pointed out the great differences between Coprothermobacter and other members of the Firmicutes, revealing that it constitutes a new deep branching lineage. Over the years, several studies based on 16S rRNA gene and whole genome sequences have indicated that Coprothermobacter is very distant phylogenetically to all other bacteria, supporting its placement in a distinct deeply rooted novel phylum...
March 29, 2018: International Journal of Systematic and Evolutionary Microbiology
Marinella Silva Laport
BACKGROUND: It is known that sponge-associated bacteria are an attractive source of new bioactive substances with biotechnological potential. These include antimicrobials, enzymes and surfactants. However, the potential of these microorganisms remains little investigated due to the difficulty of isolating new bacterial groups that produce original bioactive metabolites and enzymes. METHODS: Cultivation methods are still playing crucial functions in many studies involving bacteria isolated from sponges, and in the traditional approach for biodiscovery by screening culture collections...
March 28, 2018: Current Pharmaceutical Biotechnology
Anne-Catherine Portmann, Coralie Fournier, Johan Gimonet, Catherine Ngom-Bru, Caroline Barretto, Leen Baert
Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations. Despite its increased use, no standards or guidelines are available today for the use of WGS in outbreak and/or trace-back investigations...
2018: Frontiers in Microbiology
Marina Sánchez-Hidalgo, Ignacio González, Cristian Díaz-Muñoz, Germán Martínez, Olga Genilloud
Actinomycetes have been extensively exploited as one of the most prolific secondary metabolite-producer sources and continue to be in the focus of interest in the constant search of novel bioactive compounds. The availability of less expensive next generation genome sequencing techniques has not only confirmed the extraordinary richness and broad distribution of silent natural product biosynthetic gene clusters among these bacterial genomes, but also has allowed the incorporation of genomics in bacterial taxonomy and systematics...
2018: Frontiers in Microbiology
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